Microgreens have become increasingly popular since their introduction in the early 1990s. Their use has expanded from that of a simple garnish to an important source of phytonutrients. Microgreens are produced for fresh-cut distribution or adhered to their growing media for harvest by the end-user. Species may be selected for aesthetics or for distinctive flavor characteristics. In a recent series of studies performed to evaluate the horticultural characteristics and volatile compounds associated with flavor, microgreens were produced using a hydroponic channel mat system under greenhouse conditions. Of the twenty-one microgreen varieties evaluated, three developed fungal diseases resulting in a loss of production. Red orach (Atriplex hortensis) seed rot was caused by Penicillium spp. and Rhizopus stolonifera. Loss of cilantro (Coriandrum sativum) was associated with seed infected by R. stolonifera and damping-off of basil (Ocimum basilicum) resulted from Rhizoctonia solani. In a pilot study using arugula (Eruca sativa), mustard (Brassica juncea), and anise (Pimpinella anisum), potential seed disinfestation treatments, acetic acid, hydrogen peroxide, peracetic acid, clove oil, and thymol were evaluated for their impact on microgreen germination and productivity. Acetic acid had no detrimental impact on biomass accumulation for arugula and mustard. All other treatments had a negative impact on arugula biomass production, while thymol and clove oil reduced mustard microgreen harvest weights. Anise germination was poor regardless of treatment.